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    UPF2 UPF2, regulator of nonsense mediated mRNA decay [ Homo sapiens (human) ]

    Gene ID: 26019, updated on 19-May-2017
    Official Symbol
    UPF2provided by HGNC
    Official Full Name
    UPF2, regulator of nonsense mediated mRNA decayprovided by HGNC
    Primary source
    HGNC:HGNC:17854
    See related
    Ensembl:ENSG00000151461 MIM:605529; Vega:OTTHUMG00000017678
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    HUPF2; RENT2; smg-3
    Summary
    This gene encodes a protein that is part of a post-splicing multiprotein complex involved in both mRNA nuclear export and mRNA surveillance. mRNA surveillance detects exported mRNAs with truncated open reading frames and initiates nonsense-mediated mRNA decay (NMD). When translation ends upstream from the last exon-exon junction, this triggers NMD to degrade mRNAs containing premature stop codons. This protein is located in the perinuclear area. It interacts with translation release factors and the proteins that are functional homologs of yeast Upf1p and Upf3p. Two splice variants have been found for this gene; both variants encode the same protein. [provided by RefSeq, Jul 2008]
    Orthologs
    Location:
    10p14
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 10 NC_000010.11 (11920022..12043170, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (11962021..12085169, complement)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376415 Neighboring gene proline and serine rich 2 Neighboring gene PROSER2 antisense RNA 1 Neighboring gene RNA, U6 small nuclear 1095, pseudogene Neighboring gene uncharacterized LOC105376416 Neighboring gene dehydrogenase E1 and transketolase domain containing 1 Neighboring gene RNA, U6 small nuclear 88, pseudogene

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    NHGRI GWAS Catalog

    Description
    A genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants.
    NHGRI GWA Catalog
    • Exon junction complex (EJC), organism-specific biosystem (from KEGG)
      Exon junction complex (EJC), organism-specific biosystemStructural complex; Genetic information processing; RNA processing
    • Exon junction complex (EJC), conserved biosystem (from KEGG)
      Exon junction complex (EJC), conserved biosystemStructural complex; Genetic information processing; RNA processing
    • Gene Expression, organism-specific biosystem (from REACTOME)
      Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
    • Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC), organism-specific biosystem (from REACTOME)
      Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC), organism-specific biosystemDuring normal translation termination eRF3 associates with the ribosome and then interacts with PABP bound to the polyadenylate tail of the mRNA to release the ribosome and allow a new round of trans...
    • Nonsense-Mediated Decay (NMD), organism-specific biosystem (from REACTOME)
      Nonsense-Mediated Decay (NMD), organism-specific biosystemThe Nonsense-Mediated Decay (NMD) pathway activates the destruction of mRNAs containing premature termination codons (PTCs) (reviewed in Isken and Maquat 2007, Chang et al. 2007, Behm-Ansmant et al. ...
    • RNA transport, organism-specific biosystem (from KEGG)
      RNA transport, organism-specific biosystemRNA transport from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes (NPCs) ...
    • RNA transport, conserved biosystem (from KEGG)
      RNA transport, conserved biosystemRNA transport from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes (NPCs) ...
    • mRNA surveillance pathway, organism-specific biosystem (from KEGG)
      mRNA surveillance pathway, organism-specific biosystemThe mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go ...
    • mRNA surveillance pathway, conserved biosystem (from KEGG)
      mRNA surveillance pathway, conserved biosystemThe mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go ...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • KIAA1408, MGC138834, MGC138835, DKFZp434D222

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    RNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    telomeric DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    animal organ regeneration IEA
    Inferred from Electronic Annotation
    more info
     
    liver development IEA
    Inferred from Electronic Annotation
    more info
     
    mRNA export from nucleus TAS
    Traceable Author Statement
    more info
    PubMed 
    nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    nuclear-transcribed mRNA catabolic process, nonsense-mediated decay TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    P-body IDA
    Inferred from Direct Assay
    more info
     
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytosol IDA
    Inferred from Direct Assay
    more info
     
    cytosol TAS
    Traceable Author Statement
    more info
     
    exon-exon junction complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    perinuclear region of cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    polysome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Preferred Names
    regulator of nonsense transcripts 2
    Names
    UPF2 regulator of nonsense transcripts homolog
    nonsense mRNA reducing factor 2
    smg-3 homolog, nonsense mediated mRNA decay factor
    up-frameshift suppressor 2 homolog
    yeast Upf2p homolog

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_033936.1 RefSeqGene

      Range
      5001..128149
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_015542.3NP_056357.1  regulator of nonsense transcripts 2

      See identical proteins and their annotated locations for NP_056357.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains a different 5' UTR than variant 1 and is the shorter transcript.
      Source sequence(s)
      AF301013, BC114964, DA188353
      Consensus CDS
      CCDS7086.1
      UniProtKB/Swiss-Prot
      Q9HAU5
      Related
      ENSP00000350221.5, OTTHUMP00000019092, ENST00000357604.9, OTTHUMT00000046784
      Conserved Domains (3) summary
      smart00543
      Location:773986
      MIF4G; Middle domain of eukaryotic initiation factor 4G (eIF4G)
      pfam04050
      Location:10951218
      Upf2; Up-frameshift suppressor 2
      cl19727
      Location:358421
      DUF1451; Zinc-ribbon containing domain
    2. NM_080599.2NP_542166.1  regulator of nonsense transcripts 2

      See identical proteins and their annotated locations for NP_542166.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) contains a different 5' UTR than variant 2 and is the longer transcript.
      Source sequence(s)
      AF301013, BC114964, DB065422
      Consensus CDS
      CCDS7086.1
      UniProtKB/Swiss-Prot
      Q9HAU5
      Related
      ENSP00000380244.2, ENST00000397053.6
      Conserved Domains (3) summary
      smart00543
      Location:773986
      MIF4G; Middle domain of eukaryotic initiation factor 4G (eIF4G)
      pfam04050
      Location:10951218
      Upf2; Up-frameshift suppressor 2
      cl19727
      Location:358421
      DUF1451; Zinc-ribbon containing domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000010.11 Reference GRCh38.p7 Primary Assembly

      Range
      11920022..12043170 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017016034.1XP_016871523.1  regulator of nonsense transcripts 2 isoform X1

    2. XM_011519449.2XP_011517751.1  regulator of nonsense transcripts 2 isoform X2

      Conserved Domains (2) summary
      smart00543
      Location:168363
      MIF4G; Middle domain of eukaryotic initiation factor 4G (eIF4G)
      cl19727
      Location:358421
      DUF1451; Zinc-ribbon containing domain

    RNA

    1. XR_930489.2 RNA Sequence

    Alternate CHM1_1.1

    Genomic

    1. NC_018921.2 Alternate CHM1_1.1

      Range
      11961725..12085128 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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